data_D3Z
# 
_chem_comp.id                                    D3Z 
_chem_comp.name                                  "1-(5-deoxy-beta-L-xylofuranosyl)pyrimidine-2,4(1H,3H)-dione" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C9 H12 N2 O5" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2008-05-14 
_chem_comp.pdbx_modified_date                    2011-06-04 
_chem_comp.pdbx_ambiguous_flag                   N 
_chem_comp.pdbx_release_status                   REL 
_chem_comp.pdbx_replaced_by                      ? 
_chem_comp.pdbx_replaces                         ? 
_chem_comp.formula_weight                        228.202 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     D3Z 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        Corina 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        3D3Z 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
# 
loop_
_chem_comp_atom.comp_id 
_chem_comp_atom.atom_id 
_chem_comp_atom.alt_atom_id 
_chem_comp_atom.type_symbol 
_chem_comp_atom.charge 
_chem_comp_atom.pdbx_align 
_chem_comp_atom.pdbx_aromatic_flag 
_chem_comp_atom.pdbx_leaving_atom_flag 
_chem_comp_atom.pdbx_stereo_config 
_chem_comp_atom.model_Cartn_x 
_chem_comp_atom.model_Cartn_y 
_chem_comp_atom.model_Cartn_z 
_chem_comp_atom.pdbx_model_Cartn_x_ideal 
_chem_comp_atom.pdbx_model_Cartn_y_ideal 
_chem_comp_atom.pdbx_model_Cartn_z_ideal 
_chem_comp_atom.pdbx_component_atom_id 
_chem_comp_atom.pdbx_component_comp_id 
_chem_comp_atom.pdbx_ordinal 
D3Z N1     N1     N 0 1 N N N 32.046 28.577 -6.031 0.793  0.223  -0.423 N1     D3Z 1  
D3Z C2     C2     C 0 1 N N N 30.916 28.488 -5.195 1.307  -0.985 -0.129 C2     D3Z 2  
D3Z N3     N3     N 0 1 N N N 30.343 29.601 -4.747 2.599  -1.120 0.224  N3     D3Z 3  
D3Z C4     C4     C 0 1 N N N 30.814 30.810 -5.055 3.402  -0.038 0.287  C4     D3Z 4  
D3Z C5     C5     C 0 1 N N N 31.914 30.903 -5.866 2.874  1.239  -0.020 C5     D3Z 5  
D3Z C6     C6     C 0 1 N N N 32.534 29.763 -6.359 1.574  1.345  -0.371 C6     D3Z 6  
D3Z O2     O2     O 0 1 N N N 30.433 27.384 -4.867 0.595  -1.969 -0.182 O2     D3Z 7  
D3Z O4     O4     O 0 1 N N N 30.282 31.864 -4.649 4.571  -0.159 0.607  O4     D3Z 8  
D3Z "C1'"  "C1'"  C 0 1 N N S 32.697 27.389 -6.522 -0.616 0.337  -0.810 "C1'"  D3Z 9  
D3Z "C2'"  "C2'"  C 0 1 N N S 32.362 26.298 -5.526 -1.371 1.254  0.178  "C2'"  D3Z 10 
D3Z "O2'"  "O2'"  O 0 1 N N N 31.487 25.331 -6.135 -1.493 2.573  -0.356 "O2'"  D3Z 11 
D3Z "C3'"  "C3'"  C 0 1 N N S 33.694 25.751 -5.044 -2.762 0.594  0.313  "C3'"  D3Z 12 
D3Z "C4'"  "C4'"  C 0 1 N N S 34.778 26.507 -5.791 -2.682 -0.643 -0.609 "C4'"  D3Z 13 
D3Z "O3'"  "O3'"  O 0 1 N N N 33.851 25.971 -3.652 -2.998 0.196  1.665  "O3'"  D3Z 14 
D3Z "O4'"  "O4'"  O 0 1 N N N 34.125 27.564 -6.521 -1.273 -0.944 -0.700 "O4'"  D3Z 15 
D3Z "C5'"  "C5'"  C 0 1 N N N 35.812 27.029 -4.800 -3.439 -1.819 0.011  "C5'"  D3Z 16 
D3Z HN3    HN3    H 0 1 N N N 29.535 29.529 -4.162 2.954  -1.998 0.434  HN3    D3Z 17 
D3Z H5     H5     H 0 1 N N N 32.304 31.876 -6.125 3.502  2.116  0.025  H5     D3Z 18 
D3Z H6     H6     H 0 1 N N N 33.400 29.842 -6.999 1.154  2.311  -0.609 H6     D3Z 19 
D3Z "H1'"  "H1'"  H 0 1 N N N 32.369 27.157 -7.546 -0.700 0.723  -1.826 "H1'"  D3Z 20 
D3Z "H2'"  "H2'"  H 0 1 N N N 31.800 26.656 -4.651 -0.863 1.278  1.142  "H2'"  D3Z 21 
D3Z "HO2'" "HO2'" H 0 0 N N N 31.294 25.595 -7.027 -1.960 3.191  0.223  "HO2'" D3Z 22 
D3Z "H3'"  "H3'"  H 0 1 N N N 33.750 24.668 -5.228 -3.542 1.275  -0.028 "H3'"  D3Z 23 
D3Z "H4'"  "H4'"  H 0 1 N N N 35.322 25.864 -6.498 -3.085 -0.408 -1.594 "H4'"  D3Z 24 
D3Z "HO3'" "HO3'" H 0 0 N N N 33.886 25.136 -3.201 -3.858 -0.224 1.807  "HO3'" D3Z 25 
D3Z "H5'"  "H5'"  H 0 1 N N N 36.779 27.155 -5.310 -4.485 -1.546 0.148  "H5'"  D3Z 26 
D3Z "H5'A" "H5'A" H 0 0 N N N 35.480 27.998 -4.400 -3.373 -2.683 -0.651 "H5'A" D3Z 27 
D3Z "H5'B" "H5'B" H 0 0 N N N 35.924 26.310 -3.975 -2.998 -2.067 0.976  "H5'B" D3Z 28 
# 
loop_
_chem_comp_bond.comp_id 
_chem_comp_bond.atom_id_1 
_chem_comp_bond.atom_id_2 
_chem_comp_bond.value_order 
_chem_comp_bond.pdbx_aromatic_flag 
_chem_comp_bond.pdbx_stereo_config 
_chem_comp_bond.pdbx_ordinal 
D3Z N1    C2     SING N N 1  
D3Z N1    C6     SING N N 2  
D3Z N1    "C1'"  SING N N 3  
D3Z C2    N3     SING N N 4  
D3Z C2    O2     DOUB N N 5  
D3Z N3    C4     SING N N 6  
D3Z C4    C5     SING N N 7  
D3Z C4    O4     DOUB N N 8  
D3Z C5    C6     DOUB N N 9  
D3Z "C1'" "C2'"  SING N N 10 
D3Z "C1'" "O4'"  SING N N 11 
D3Z "C2'" "O2'"  SING N N 12 
D3Z "C2'" "C3'"  SING N N 13 
D3Z "C3'" "C4'"  SING N N 14 
D3Z "C3'" "O3'"  SING N N 15 
D3Z "C4'" "O4'"  SING N N 16 
D3Z "C4'" "C5'"  SING N N 17 
D3Z N3    HN3    SING N N 18 
D3Z C5    H5     SING N N 19 
D3Z C6    H6     SING N N 20 
D3Z "C1'" "H1'"  SING N N 21 
D3Z "C2'" "H2'"  SING N N 22 
D3Z "O2'" "HO2'" SING N N 23 
D3Z "C3'" "H3'"  SING N N 24 
D3Z "C4'" "H4'"  SING N N 25 
D3Z "O3'" "HO3'" SING N N 26 
D3Z "C5'" "H5'"  SING N N 27 
D3Z "C5'" "H5'A" SING N N 28 
D3Z "C5'" "H5'B" SING N N 29 
# 
loop_
_pdbx_chem_comp_descriptor.comp_id 
_pdbx_chem_comp_descriptor.type 
_pdbx_chem_comp_descriptor.program 
_pdbx_chem_comp_descriptor.program_version 
_pdbx_chem_comp_descriptor.descriptor 
D3Z SMILES           ACDLabs              10.04 "O=C1NC(=O)N(C=C1)C2OC(C(O)C2O)C"                                                                                     
D3Z SMILES_CANONICAL CACTVS               3.341 "C[C@@H]1O[C@@H]([C@@H](O)[C@@H]1O)N2C=CC(=O)NC2=O"                                                                   
D3Z SMILES           CACTVS               3.341 "C[CH]1O[CH]([CH](O)[CH]1O)N2C=CC(=O)NC2=O"                                                                           
D3Z SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C[C@H]1[C@H]([C@@H]([C@H](O1)N2C=CC(=O)NC2=O)O)O"                                                                    
D3Z SMILES           "OpenEye OEToolkits" 1.5.0 "CC1C(C(C(O1)N2C=CC(=O)NC2=O)O)O"                                                                                     
D3Z InChI            InChI                1.03  "InChI=1S/C9H12N2O5/c1-4-6(13)7(14)8(16-4)11-3-2-5(12)10-9(11)15/h2-4,6-8,13-14H,1H3,(H,10,12,15)/t4-,6+,7-,8-/m0/s1" 
D3Z InChIKey         InChI                1.03  WUBAOANSQGKRHF-UCVXFZOQSA-N                                                                                           
# 
loop_
_pdbx_chem_comp_identifier.comp_id 
_pdbx_chem_comp_identifier.type 
_pdbx_chem_comp_identifier.program 
_pdbx_chem_comp_identifier.program_version 
_pdbx_chem_comp_identifier.identifier 
D3Z "SYSTEMATIC NAME" ACDLabs              10.04 "1-(5-deoxy-beta-L-xylofuranosyl)pyrimidine-2,4(1H,3H)-dione"              
D3Z "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "1-[(2S,3S,4S,5S)-3,4-dihydroxy-5-methyl-oxolan-2-yl]pyrimidine-2,4-dione" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
D3Z "Create component"  2008-05-14 RCSB 
D3Z "Modify descriptor" 2011-06-04 RCSB 
# 
